Substrate recognition by norovirus polymerase: microsecond molecular dynamics study
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11320%2F13%3A10190059" target="_blank" >RIV/00216208:11320/13:10190059 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.1007/s10822-013-9652-8" target="_blank" >http://dx.doi.org/10.1007/s10822-013-9652-8</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1007/s10822-013-9652-8" target="_blank" >10.1007/s10822-013-9652-8</a>
Alternative languages
Result language
angličtina
Original language name
Substrate recognition by norovirus polymerase: microsecond molecular dynamics study
Original language description
Molecular dynamics simulations of complexes between Norwalk virus RNA dependent RNA polymerase and its natural CTP and 2dCTP (both containing the O5'-C5'-C4'-O4' sequence of atoms bridging the triphosphate and sugar moiety) or modified coCTP (C5'-O5'-C4'-O4'), cocCTP (C5'-O5'-C4'-C4 '') substrates were produced by means of CUDA programmable graphical processing units and the ACEMD software package. It enabled us to gain microsecond MD trajectories clearly showing that similar nucleoside triphosphates can bind surprisingly differently into the active site of the Norwalk virus RNA dependent RNA polymerase. It corresponds to their different modes of action (CTP-substrate, 2dCTP-poor substrate, coCTP-chain terminator, cocCTP-inhibitor). Moreover, extremelyrare events-as repetitive pervasion of Arg182 into a potentially reaction promoting arrangement-were captured.
Czech name
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Czech description
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Classification
Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
BO - Biophysics
OECD FORD branch
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Result continuities
Project
<a href="/en/project/GA202%2F09%2F0193" target="_blank" >GA202/09/0193: Formation and dynamics of nucleic acid motifs involved in regulation of gene expression</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2013
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Computer-Aided Molecular Design
ISSN
0920-654X
e-ISSN
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Volume of the periodical
27
Issue of the periodical within the volume
4
Country of publishing house
NL - THE KINGDOM OF THE NETHERLANDS
Number of pages
16
Pages from-to
373-388
UT code for WoS article
000320505600007
EID of the result in the Scopus database
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